Comparison of proteases in DNA extraction via quantitative polymerase chain reaction

Eychner, Alison M.; Lebo, Roberta J.; Elkins, Kelly M.

doi:10.1016/j.ab.2014.08.030

Cited by 9 publications

(6 citation statements)

References 11 publications

(10 reference statements)

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“…In recent decades, biomedical research has advanced much of our understanding of the biological function of proteases, revealing the mechanisms associated with their digestion and breakdown of proteins into small fragments via the severing of peptide bonds 1–3 . Furthermore, a number of studies established that proteases can be used in a large number of biotechnological applications, including DNA extraction 4 , control of signaling pathways 5, 6 , and infection and manipulation of pathogens 7 . Given the diversity of their functional roles, proteases are also implicated in a number of human diseases.…”

Section: Introductionmentioning

confidence: 99%

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Wang

Song

Marquez‐Lago

et al. 2017

Sci Rep

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Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.

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Section: Introductionmentioning

confidence: 99%

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Wang

Song

Marquez‐Lago

et al. 2017

Sci Rep

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“…We also obtained a ten times higher yield with raw milk, as described by Eichner et al. . A comparison study is necessary to validate our first results with the gold‐standard genotyping technique, this time using blood samples.…”

Section: Ibuprofen Rid and Genotype Profil (N = 13 Breastfeeding Women)mentioning

confidence: 82%

“…Hass et al (10) obtained a quantifiable amount of DNA from pasteurised and unpasteurised samples with better amplification from untreated milk. We also obtained a ten times higher yield with raw milk, as described by Eichner et al (11). A comparison study is necessary to validate our first results with the gold-standard genotyping technique, this time using blood samples.…”

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confidence: 82%

Rapid and sensitive analysis of polymorphisms from breastmilk shows that ibuprofen is safe during certain stages of breastfeeding

Rigourd¹,

Méritet

Seraissol

et al. 2015

Acta Paediatr

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Ibuprofen is a commonly used analgesic and second therapeutic class prescribed at different stages of lactation (1). We previously published a study about 20 women who received a mean daily dose of 1.012 mg (AE96 mg) of ibuprofen to treat pain or inflammatory disorders (2). Ibuprofen milk concentrations were measured using high-performance liquid chromatography, and the mean concentration was 360 AE 160 lg/L. The mean ibuprofen transfer infant dose was 68 (8-262) lg/kg/day and the relative infant dose was <0.38% (0.04-1.53) of the weight-adjusted maternal daily dose, which was equal to 0.2% of the paediatric dose. Our advice is that ibuprofen is safe in the post-partum and later post-partum periods because the relative infant dose is very low in colostrum or mature milk. When Townsend et al. studied ibuprofen transfer in colostrum and Rigourd et al. studied it in mature milk, the relative infant dose was always under 1% (2,3). Our current belief is that there are sufficient pharmacokinetic data to confirm that there is a very poor transfer of ibuprofen from the mother's milk to the neonate. We have concluded that the use of ibuprofen is compatible with breastfeeding after the early post-partum stage and with prolonged breastfeeding (2).Codeine, like ibuprofen, is often used as antalgic during the post-partum period. However, recent data have shown that codeine could trigger serious adverse events, even neonatal death (3,4), during breastfeeding. In contrast, ibuprofen did not show any adverse events. Codeine is fully metabolised by cytochrome 2D6, while ibuprofen is partially metabolised by CY2C8 (5) and preferentially metabolised by CYP2C9 (6).We studied the cytochrome P450 enzymes involved in ibuprofen metabolism: CYP2C8 and CYP2C9. DNA was extracted from 13 frozen breastmilk samples in 1-mL aliquots, using the Qiagen Kit (QiaSymphony DSP DNA; Qiagen, Courtaboeuf France). All the DNA was amplified by screening with taqman technology for cytochrome P450 polymorphism. Genotype analysis was carried out for cytochromes CYP 2C8 and CYP2C9. All laboratory procedures were performed in accordance with the local ethics committee (CPP Ile de France) and pharmacogenetics standard operating laboratory procedures at Paris South University's School of Medicine. The chi-square test was used to compare the genotype frequencies and the associations with CYP2C8 and CYP2C9.We obtained a sufficient concentration of good-quality DNA (Table 1). Allelic variants were present in the same proportion as in the Caucasian population. For every genetic polymorphism, the relative infant dose of ibuprofen was less than 1.56%.These polymorphisms determine the pharmacokinetics of ibuprofen. Interindividual variability in drug metabolism is a major cause of adverse drug effects, and in nonsteroidal anti-inflammatory drugs (NSAIDs), this variability is linked to polymorphisms in genes coding for drug-metabolising enzymes. Both CYP2C8 and CYP2C9 contribute equally to the metabolism of ibuprofen (7). The main CYP2C9 polymorphisms responsible for t...

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“…The lack of statistical significance in the DNA recovery value differences is likely attributed to the small sample size and large variation within each region and within donors. Great variation in small sample sizes has been observed in other DNA recovery studies as well [23,24]. In addition, no correlation was observed between the quantity of DNA recovered and the completeness of the STR profile below one nanogram of DNA.…”

Section: F I G U R Ementioning

confidence: 87%

Comparison of DNA yield and STR profiles from the diaphysis, mid‐diaphysis, and metaphysis regions of femur and tibia long bones

Klavens

Kollmann

Elkins

et al. 2020

Journal of Forensic Sciences

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DNA testing of human bones is performed for identification when there is no remaining soft tissue, which often means the samples are old or environmentally compromised. Under these circumstances, it can be difficult to obtain a STR DNA profile. It is important to recover the highest quantity and quality of DNA for STR typing. This How to cite this article: Klavens A, Kollmann DD, Elkins KM, Zeller CB. Comparison of DNA yield and STR profiles from the diaphysis, mid-diaphysis, and metaphysis regions of femur and tibia long bones.

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Comparison of proteases in DNA extraction via quantitative polymerase chain reaction

Cited by 9 publications

References 11 publications

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Rapid and sensitive analysis of polymorphisms from breastmilk shows that ibuprofen is safe during certain stages of breastfeeding

Comparison of DNA yield and STR profiles from the diaphysis, mid‐diaphysis, and metaphysis regions of femur and tibia long bones

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